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PubMed2005

Approaches to the analysis of cell signaling networks and their application in drug discovery.

The ability to predict the safety and efficacy of novel drugs prior to clinical testing is a key goal in pharmaceutical drug discovery. Gaining a mechanistic understanding of the complex cell signaling networks (CSNs) underlying disease processes promises to help reduce the number of clinical failures by identifying points of intervention as well as redundancies and feedback mechanisms that contribute to toxicities, lack of efficacy and unexpected biological activities. Experimental and computational approaches to analyzing and modeling CSNs are currently being validated using simple organisms and cell lines. In vitro cell systems of sufficient complexity to resemble human disease physiology, but which are also amenable to chemical and genetic perturbations on a large scale, are now required for deciphering the signaling networks operating in human disease. In this review, experimental and computational methods for modeling complex CSNs and the applications of these approaches to pharmaceutical drug discovery are discussed.

Animals↗
PubMed1990

[Stereological analysis of the vascular network of the ganglionic eminence and the corpus striatum during brain development in man].

A study of the volume density of the ganglionic eminence vascular network and the constituent parts of the corpus striatum was performed on 8 chosen foetal brains, which were well-injected with a mixture of India ink and gelatin, aged from 14-25 postovulatory weeks. The volume density of the ganglionic eminence vascular network amounts to 0.0209-0.0300 mm0, of the caudate nucleus to 0.0131-0.0181 mm0, of the putamen to 0.0136-0.0159 mm0, and of the globus pallidus to 0.0121-0.0159 mm0. The comparison of the results obtained, shows that the volume density of the ganglionic eminence vascular network is higher than the volume density of the other examined structures and that this difference is statistically highly significant (p less than 0.01). The augmented volume density of the ganglionic eminence vascular network points to a possibility of slow blood flow through its vascular bed, which was experimentally demonstrated on animals. This slow blood flow, among other factors, may be the cause of a ganglionic eminence venous infarction in premature newborns of low birthweight.

Corpus Striatum↗
PubMed1990

[Morphometric analysis of the vascular network of the suprachiasmatic and paraventricular nucleus in the human brain].

The aim of the study is to discover, the sources of vascularization, vascular areas, the size and density of the capillary network in the suprachiasmatic and the paraventricular nuclei of postnatal human brains of both sexes. The brain blood vessels under examination were filled with a mixture of India ink and gelatin. The serial paraffin sections of 200 microns cleared after Spalteholz. In the vascularization of the suprachiasmatic and the paraventricular nuclei, two arterial stems, take part with their branches (a. cerebri anterior and a. communicans anterior). In order to quantify the density of the capillary network, the authors used the standard stereologic parameters - volume density, surface density and mean radius of blood vessels. The comparative testing of the mean values obtained in male and female subjects did not reveal any significant sex - dependent differences regarding the size and density of the capillary network in the suprachiasmatic and the paraventricular nuclei of the human brain.

Capillaries↗
PubMed1987

Analysis of the idiotypic network in tumor immunity.

Herein we have analyzed the expression of idiotopes associated with a monoclonal anti-tumor-associated antigen (TAA) antibody in DBA/2 mice which have progressively growing tumors or resist tumor growth. A panel of eight monoclonal antiidiotypic antibodies raised against a monoclonal antibody which reacts with a mouse mammary tumor virus cross-reactive qp52 envelope protein (TAA) of the L1210/GZL lymphoma was used to measure the expression of idiotopes in sera from different treatment groups. Significant correlations between the expression of certain idiotopes and the growth of the tumor or the establishment of anti-tumor immunity are seen. 1) Idiotypes detected by anti-idiotype D11 are high in anti-idiotype immunized progressor or tumor-susceptible mice and low or absent in regressor mice, i.e., the mice immunized with the protective 2F10 anti-idiotype; 2) the 3A4-detected idiotypes are less frequent or absent in irradiated tumor-immunized regressor mice than in untreated mice challenged with live tumor or progressor mice; 3) no difference in the anti-TAA titers is seen in mice in which the tumor growth is inhibited and in mice in which the tumor grows; 4) no difference in 11C1 idiotype + anti-TAA titer was observed between regressor and progressor mice; and 5) mice with normal or accelerated tumor growth have higher titers of idiotypes detected by a polyclonal anti-idiotype. These findings provide evidence for a regulatory idiotype network induced by the growing L1210/GZL tumor or by anti-idiotypic immunization. The titer of anti-TAA antibody does not correlate with the biology of tumor growth, but certain idiotopes correlate with either progressive or regressive tumor behavior. Therefore, the target of the idiotype regulation is likely to be anti-tumor T effector cells. Effective idiotype therapy of tumors must deal with the complexity of idiotype regulation induced by the tumor itself and is unlikely to be successful if anti-idiotypes are used only as internal mimicry of a TAA.

Animals↗
PubMed1995

Molecular analysis of the cytokine network involved in cachexia in colon 26 adenocarcinoma-bearing mice.

Two clones, one cachexigenic (clone 20) and the other noncachexigenic (clone 5), from a murine colon adenocarcinoma, colon 26 cells, were used to analyze the involvement of immune reactions as well as the cytokine network in cachexia. Clone 20 induced cachexia in nude and SCID mice as well as in normal BALB/c mice, suggesting that lymphocytes played little, if any, role in the process. Both clones failed to express mRNA of interleukin (IL) 1 alpha, IL-1 beta, IL-6, and tumor necrosis factor alpha in vitro with or without the coculture of NIH3T3 cells or spleen cells. However, IL-6 mRNA was selectively detected at the tumor site of clone 20 but not at that of clone 5-bearing mice. In contrast, tumor necrosis factor alpha mRNA was detected at tumor sites and in spleens of only clone 5-bearing mice, suggesting a potential role of IL-6, but not tumor necrosis factor alpha, in inducing cachexia. Anti-IL-6 antibody partially reversed the weight loss induced by clone 20, whereas the continuous infusion of IL-6 failed to cause weight loss, despite being associated with an elevation of a serum acute phase protein. These results suggest that IL-6 is necessary but not sufficient for the induction of cachexia. Both clones expressed IL-6 mRNA in the presence of IL-1 in vitro, and mice bearing either clone expressed IL-1 beta mRNA at the tumor site. Moreover, IL-1 receptor antagonist (IL-1Ra) mRNA was detected at the tumor site of clone 5-bearing mice but not at that of clone 20-bearing mice, suggesting that IL-1Ra might block IL-1 activity to reduce IL-6 production in clone 5-bearing mice. However, the transfection of clone 20 with IL-1Ra cDNA failed to abolish its capacity to produce IL-6 and to cause cachexia. Collectively, additional factor(s) besides IL-1Ra and IL-1 beta may control IL-6 and some other cachexigenic factor production, thereby causing cachexia in this model.

Adenocarcinoma↗
PubMed1998

Analysis of the cytokine network among tumor necrosis factor alpha, interleukin-1beta, interleukin-8, and interleukin-1 receptor antagonist in monosodium urate crystal-induced rabbit arthritis.

In the present study, we analyzed the cytokine network among TNFalpha, IL-1beta, IL-8, and IL-1 receptor antagonist (IL-1Ra) in a rabbit experimental model of acute gout. The production of TNFalpha in synovial fluids reached the peak at 2 hours after the intra-articular injection of monosodium urate (MSU) crystals. The production of IL-1beta and IL-8 reached the first peak at 2 hours and the second peak at 9 and 12 hours, respectively. The production of endogenous IL-1Ra reached the peak at 9 hours. The source of TNFalpha and the first phase of IL-8 was synovial cells, whereas infiltrating leukocytes were the source of the second phase of IL-8 and also of IL-1beta and IL-1Ra. The production of TNFalpha was not altered by either anti-lL-8 IgG or IL-1Ra. The first IL-1beta peak was reduced only with a combination of anti-TNFalpha mAb and anti-lL-8 IgG, whereas the second peak was significantly reduced by either inhibitor. The first IL-8 peak was not altered with anti-TNFalpha mAb or IL-1 Ra, whereas the second IL-8 peak was reduced with IL-1Ra. Anti-TNFalpha mAb or anti-lL-8 IgG significantly reduced the peak level of endogenous IL-1Ra. These cytokine inhibitors also attenuated the maximal leukocyte accumulation at 9 hours, but not the initial phase, which occurred within 2 hours. These results provide evidence that IL-8 and TNFalpha were responsible for the production of IL-1beta and IL-1Ra, and that IL-1beta was responsible for the second phase of IL-1beta and IL-8 production. Our data also suggest that the initial and the maximal phases of leukocyte influx are differently regulated. Finally, the intravenous injection of colchicine inhibited neutrophil infiltration without affecting the production of TNFalpha or the first peak of IL-8, suggesting that colchicine inhibits MSU crystal-induced arthritis by directly inhibiting the migration of neutrophils.

Animals↗
PubMed1998

Functional analysis of the PTH/PTHrP network of ligands and receptors.

Parathyroid hormone (PTH) and parathyroid hormone-related protein (PTHrP) are two related proteins that activate a common PTH/PTHrP receptor, yet have quite distinct physiologic missions. PTH is the major peptide regulator of blood calcium in higher vertebrates, while PTHrP predominantly acts as a paracrine regulator of differentiation and local intercellular signaling. To analyze the physiological roles of PTHrP and the PTH/PTHrP receptor, "knockout" mice missing either the PTHrP or the PTH/PTHrP receptor gene were developed. Both the PTHrP (-/-) mice and the PTH/PTHrP receptor (-/-) mice exhibit a growth plate chondrodysplasia that reflects accelerated differentiation of proliferating chondrocytes. Growth plate chondrocytes regulate the local production of PTHrP by secreting the protein, Indian hedgehog (Ihh), as they are leaving the proliferative pool. Ihh stimulates the production of PTHrP, which then slows the differentiation of chondrocytes, thereby delaying the production of Ihh. PTHrP also stimulates transport of calcium across the placenta. PTHrP (-/-) mice lack the normal elevation of fetal blood calcium (when compared to maternal levels) and have low placental transport of calcium. Fragments of PTHrP that do not bind to the PTH/PTHrP receptor can correct the defect of placental calcium transport in these mice. Thus, this action of PTHrP is not mediated by the PTH/PTHrP receptor. The "knockout" mice thus help delineate the roles of PTH. PTHrP, and the PTH/PTHrP receptor in an interacting network of ligands and receptors.

Animals↗
PubMed2003

Connective molecular pathways of experimental bladder inflammation.

Inflammation is an inherent response of the organism that permits its survival despite constant environmental challenges. The process normally leads to recovery from injury and to healing. However, if targeted destruction and assisted repair are not properly phased, chronic inflammation can result in persistent tissue damage. To better understand the inflammatory process, we recently introduced a profiling methodology to identify common genes involved in bladder inflammation. The method represents a complementation to the classic quantification of inflammation and provides information regarding the early, intermediate, and late events in gene regulation. However, gene profiling fails to describe the molecular pathways and their interconnections involved in the particular inflammatory response. The present work introduces a new statistical technique for inferring functional interconnections between inflammatory pathways underlying classic models of bladder inflammation and permits the modeling of the inflammatory network. This new statistical method is based on variants of cluster analysis, Boolean networking, differential equations, Bayesian networking, and partial correlation. By applying partial correlation analysis, we developed mosaics of gene expression that permitted a global visualization of common and unique pathways elicited by different stimuli. The significance of these processes was tested from both biological and statistical viewpoints. We propose that connective mosaic may represent the necessary simplification step to visualize cDNA array results.

Animals↗
PubMed2000

Evaluation of neural network models with generalized sensitivity analysis

A sensitivity analysis method for discovering characteristic features of the input data using neural network classification models has been devised. The sensitivity is the gradient of the neural network model response function, and because neural network models are nonlinear, the gradient depends on the point where it is evaluated. Two criteria are used for measuring the sensitivity. The first criterion calculates the sensitivity or gradient of the neural network output with respect to the average of the objects that comprise each class. The second criterion measures the average sensitivity of the class objects. The sensitivity analysis was applied to temperature-constrained cascade correlation network models and evaluated with sets of synthetic data and experimental mobility spectra. The neural network models were built using temperature-constrained cascade correlation networks (TCCCNs). A weight constraint was devised for the output units of the network models. This method implements weight decay with conjugate gradient training and yields more sensitive neural network models. Temperature-constrained hidden units furnish more sensitive network models than networks without constraints. By comparing the sensitivities of the class mean input and the mean sensitivity for all the inputs of a class, the individual input variables may be assessed for linearity. If these two sensitivities for an input variable differ by a constant factor, then that variable is modeled by a simple linear relationship. If the two sensitivities vary by a nonconstant scale factor, then the variable is modeled by higher order functions in the network. The sensitivity method was used to diagnose errors in the training data, and the test for linearity indicated a TCCCN architecture that had better predictability.

Journal Article↗
PubMed1991

A local area network for medical research; planning, realization and experience.

This report focuses on the planning and realization of an interdisciplinary local area network (LAN) for medical research at the University of Heidelberg. After a detailed requirements analysis, several networks were evaluated by means of a test installation, and a cost-performance analysis was carried out. At present, the LAN connects 45 (IBM-compatible) PCs, several heterogeneous mainframes (IBM, DEC and Siemens) and provides access to the public X.25 network and to wide-area networks for research (EARN, BITNET). The network supports application software that is frequently needed in medical research (word processing, statistics, graphics, literature databases and services, etc.). Compliance with existing "official" (e.g., IEEE 802.3) and "de facto" standards (e.g., PostScript) was considered to be extremely important for the selection of both hardware and software. Customized programs were developed to improve access control, user interface and on-line help. Wide acceptance of the LAN was achieved through extensive education and maintenance facilities, e.g., teaching courses, customized manuals and a hotline service. Since requirements of clinical routine differ substantially from medical research needs, two separate networks (with a gateway in between) are proposed as a solution to optimally satisfy the users' demands.

Costs and Cost Analysis↗
PubMed2004

Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data.

The photosynthetic cyanobacterium Synechocystis sp. strain PCC 6803 uses a complex genetic program to control its physiological response to alternating light conditions. To study this regulatory program time-series experiments were conducted by exposing Synechocystis sp. to serial perturbations in light intensity. In each experiment whole-genome DNA microarrays were used to monitor gene transcription in 20-min intervals over 8- and 16-h periods. The data was analyzed using time-lagged correlation analysis, which identifies genetic interaction networks by constructing correlations between time-shifted transcription profiles with different levels of statistical confidence. These networks allow inference of putative cause-effect relationships among the organism's genes. Using light intensity as our initial input signal, we identified six groups of genes whose time-lagged profiles possessed significant correlation, or anti-correlation, with the light intensity. We expanded this network by using the average profile from each group of genes as a seed, and searching for other genes whose time-lagged profiles possessed significant correlation, or anti-correlation, with the group's average profile. The final network comprised 50 different groups containing 259 genes. Several of these gene groups possess known light-stimulated gene clusters, such as Synechocystis sp. photosystems I and II and carbon dioxide fixation pathways, while others represent novel findings in this work.

Cyanobacteria↗
PubMed2002

Hemovigilance network in France: organization and analysis of immediate transfusion incident reports from 1994 to 1998.

BACKGROUND: Hemovigilance networks have been introduced in several countries to improve knowledge of blood transfusion-related morbidity and mortality. The general organization of the French network and its results from 1994 through March 1999 are presented here. STUDY DESIGN AND METHODS: The hemovigilance network relies on blood transfusion centers and hospital correspondents, who analyze unexpected and untoward blood transfusion-related effects and transmit a Transfusion Incident Report (TIR) to a national database (Transfusion Incident Reports Electronic Data Management [GIFIT]). RESULTS: As of March 1, 1999, the GIFIT database contained 24,234 TIRs related to incidents that occurred from the start of the hemovigilance network until December 31, 1998. The network was not fully implemented until 1996; but the reporting rate seems to have since stabilized at approximately 7000 per year (2.5 reports per 1000 blood components). The highest reporting rate is observed with platelet concentrates (4.02/1000), followed by RBCs (1.71/1000) and FFP (0.34/1000). Bacterial contamination quickly appeared as a major cause of morbidity and mortality (185 cases and 18 fatalities). However, a general trend of reduction in this type of incident was observed over time, which can be attributed to adoption of several preventive measures. In contrast, major ABO mismatchings during RBC transfusion remained at a constant rate throughout this period and accounted for six fatalities. After the implementation of universal WBC reduction, some incidents known to be related to WBCs, such as nonhemolytic febrile transfusion reactions (NHFTR) and HLA immunization, were dramatically reduced. CONCLUSION: Hemovigilance is an important tool not only to analyze blood transfusion incidents, but also to measure the effects of new processes or corrective actions at a national level.

Bacterial Infections↗
PubMed2006

Visual setup of logical models of signaling and regulatory networks with ProMoT.

BACKGROUND: The analysis of biochemical networks using a logical (Boolean) description is an important approach in Systems Biology. Recently, new methods have been proposed to analyze large signaling and regulatory networks using this formalism. Even though there is a large number of tools to set up models describing biological networks using a biochemical (kinetic) formalism, however, they do not support logical models. RESULTS: Herein we present a flexible framework for setting up large logical models in a visual manner with the software tool ProMoT. An easily extendible library, ProMoT's inherent modularity and object-oriented concept as well as adaptive visualization techniques provide a versatile environment. Both the graphical and the textual description of the logical model can be exported to different formats. CONCLUSION: New features of ProMoT facilitate an efficient set-up of large Boolean models of biochemical interaction networks. The modeling environment is flexible; it can easily be adapted to specific requirements, and new extensions can be introduced. ProMoT is freely available from http://www.mpi-magdeburg.mpg.de/projects/promot/.

Animals↗
PubMed2005

Kinetic constraints for formation of steady states in biochemical networks.

The constraint-based analysis has emerged as a useful tool for analysis of biochemical networks. This work introduces the concept of kinetic constraints. It is shown that maximal reaction rates are appropriate constraints only for isolated enzymatic reactions. For biochemical networks, it is revealed that constraints for formation of a steady state require specific relationships between maximal reaction rates of all enzymes. The constraints for a branched network are significantly different from those for a cyclic network. Moreover, the constraints do not require Michaelis-Menten constants for most enzymes, and they only require the constants for the enzymes at the branching or cyclic point. Reversibility of reactions at system boundary or branching point may significantly impact on kinetic constraints. When enzymes are regulated, regulations may impose severe kinetic constraints for the formation of steady states. As the complexity of a network increases, kinetic constraints become more severe. In addition, it is demonstrated that kinetic constraints for networks with co-regulation can be analyzed using the approach. In general, co-regulation enhances the constraints and therefore larger fluctuations in fluxes can be accommodated in the networks with co-regulation. As a first example of the application, we derive the kinetic constraints for an actual network that describes sucrose accumulation in the sugar cane culm, and confirm their validity using numerical simulations.

Biochemistry↗
PubMed2006

Evaluating brain activity in obsessive-compulsive disorder: preliminary insights from a multivariate analysis.

Obsessive-compulsive disorder (OCD) has been linked to a dysfunction of brain corticostriatal networks, although functional imaging studies of OCD rarely apply network-sensitive analysis methods. In this study, we compared a univariate and a multivariate analysis of PET data in OCD patients and healthy subjects; the latter approach was considered more suitable for characterizing functional networks of brain activity. Although both methods suggested there was abnormal corticostriatal activity in OCD patients, the nature, extent and magnitude of this activity was clearly enhanced by the multivariate approach. Implications for the analysis of such studies are discussed.

Adult↗